Rebuilding with debugging symbols (icc -debug full) in gdb shows that it's dying on line 158 of homo.c: free(fbigbasis);
Changing this to QFFTWFREE(fbigbasis); fixes the problem.

I'm surprised this works because QFFTWFREE macro expands to fftwf_free, which MKL defines as: void fftwf_free(void* x) {free(x);}
So it would seem free(fbigbasis) is the same as fftwf_free(fbigbasis), but obviously not.

Am I doing something wrong in my Makefile or in my environment?
With CC=icc and CFLAGS=' -O2 -Wall', we build like this:
autoconf -o configure configure.ac
./configure --enable-mkl
make